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    TREX1 three prime repair exonuclease 1 [ Homo sapiens (human) ]

    Gene ID: 11277, updated on 12-Oct-2019

    Summary

    Official Symbol
    TREX1provided by HGNC
    Official Full Name
    three prime repair exonuclease 1provided by HGNC
    Primary source
    HGNC:HGNC:12269
    See related
    Ensembl:ENSG00000213689 MIM:606609
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CRV; AGS1; DRN3; HERNS
    Summary
    This gene encodes a nuclear protein with 3' exonuclease activity. The encoded protein may play a role in DNA repair and serve as a proofreading function for DNA polymerase. Mutations in this gene result in Aicardi-Goutieres syndrome, chilblain lupus, Cree encephalitis, and other diseases of the immune system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]
    Annotation information
    Note: GeneID 11277 was annotated as a single gene with two non-overlapping coding regions. GeneID 11277 now represents only the downstream coding region encoding three prime repair exonuclease 1. The upstream coding region is represented by geneID 84126. [29 May 2007]
    Expression
    Ubiquitous expression in spleen (RPKM 9.5), lymph node (RPKM 7.7) and 25 other tissues See more
    Orthologs

    Genomic context

    See TREX1 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (48465830..48467645)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48506919..48509044)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene plexin B1 Neighboring gene uncharacterized LOC105377077 Neighboring gene coiled-coil domain containing 51 Neighboring gene ATRIP-TREX1 readthrough Neighboring gene translation machinery associated 7 homolog Neighboring gene ATR interacting protein Neighboring gene shisa family member 5 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Neighboring gene microRNA 6823

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 replication requires TREX1 expression in human cervicovaginal explants as shown through TREX1 knockdown PubMed
    SiRNA-mediated knockdown of one of the components of the SET complex, TREX1, inhibits HIV-1 infection with significantly reduced levels of integrated HIV-1 DNA and viral production in HeLa-CD4 cells, human cervicovaginal explants or humanized mice PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Cytosolic DNA-sensing pathway, organism-specific biosystem (from KEGG)
      Cytosolic DNA-sensing pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
    • Cytosolic DNA-sensing pathway, conserved biosystem (from KEGG)
      Cytosolic DNA-sensing pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
    • Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
      Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
    • IRF3-mediated induction of type I IFN, organism-specific biosystem (from REACTOME)
      IRF3-mediated induction of type I IFN, organism-specific biosystemTANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are central regulators of type-I interferon induction during bacterial or viral infection. TBK1 was found to form complexes with...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • Regulation by TREX1, organism-specific biosystem (from REACTOME)
      Regulation by TREX1, organism-specific biosystemThree prime repair exonuclease 1 (TREX1) is a DNase type III enzyme, which targets and digests unpaired nucleotides on ssDNA and dsDNA ends through a 3'to 5' exonuclease activity (Perrino FW et al. 1...
    • Regulation of innate immune responses to cytosolic DNA, organism-specific biosystem (from REACTOME)
      Regulation of innate immune responses to cytosolic DNA, organism-specific biosystemInnate immune responses are coordinated and regulated to provide an efficient first line of defense against pathogens and at the same time to prevent host self-damage. Here we present some regulatory...
    • STING mediated induction of host immune responses, organism-specific biosystem (from REACTOME)
      STING mediated induction of host immune responses, organism-specific biosystemSTING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. In...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough ATRIP-TREX1

    Readthrough gene: ATRIP-TREX1, Included gene: ATRIP

    Homology

    Clone Names

    • DKFZp434J0310

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    3'-5' exonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    3'-5' exonuclease activity TAS
    Traceable Author Statement
    more info
    PubMed 
    3'-5'-exodeoxyribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    3'-5'-exodeoxyribonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA binding, bending IEA
    Inferred from Electronic Annotation
    more info
     
    MutLalpha complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    MutSalpha complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    WW domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    adenyl deoxyribonucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    exodeoxyribonuclease III activity IEA
    Inferred from Electronic Annotation
    more info
     
    magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding TAS
    Traceable Author Statement
    more info
    PubMed 
    protein homodimerization activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein homodimerization activity TAS
    Traceable Author Statement
    more info
    PubMed 
    single-stranded DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    CD86 biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    DNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA modification IEA
    Inferred from Electronic Annotation
    more info
     
    DNA recombination NAS
    Non-traceable Author Statement
    more info
    PubMed 
    DNA repair TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA replication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    DNA synthesis involved in UV-damage excision repair IEA
    Inferred from Electronic Annotation
    more info
     
    T cell antigen processing and presentation IEA
    Inferred from Electronic Annotation
    more info
     
    activation of immune response IEA
    Inferred from Electronic Annotation
    more info
     
    apoptotic cell clearance IEA
    Inferred from Electronic Annotation
    more info
     
    atrial cardiac muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
     
    blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to gamma radiation IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to hydroxyurea IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to interferon-beta IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to reactive oxygen species IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to virus IEA
    Inferred from Electronic Annotation
    more info
     
    detection of DNA damage stimulus involved in DNA damage checkpoint IEA
    Inferred from Electronic Annotation
    more info
     
    detection of stimulus involved in cell cycle checkpoint IEA
    Inferred from Electronic Annotation
    more info
     
    determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
     
    establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    generation of precursor metabolites and energy IEA
    Inferred from Electronic Annotation
    more info
     
    heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    heart process IEA
    Inferred from Electronic Annotation
    more info
     
    immune complex formation IEA
    Inferred from Electronic Annotation
    more info
     
    immune response in brain or nervous system IEA
    Inferred from Electronic Annotation
    more info
     
    immunoglobulin biosynthetic process involved in immune response IEA
    Inferred from Electronic Annotation
    more info
     
    inflammatory response to antigenic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    interferon-alpha production IEA
    Inferred from Electronic Annotation
    more info
     
    kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    lymphoid progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    macrophage activation involved in immune response IEA
    Inferred from Electronic Annotation
    more info
     
    mismatch repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    negative regulation of type I interferon-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    nucleic acid phosphodiester bond hydrolysis IEA
    Inferred from Electronic Annotation
    more info
     
    protein stabilization IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of T cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of catalytic activity IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cellular respiration IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of fatty acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of glycolytic process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of immunoglobulin production IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of lipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of lysosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of protein complex stability IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of tumor necrosis factor production IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of type I interferon production TAS
    Traceable Author Statement
    more info
     
    signal transduction involved in DNA damage checkpoint IEA
    Inferred from Electronic Annotation
    more info
     
    transposition, RNA-mediated IEA
    Inferred from Electronic Annotation
    more info
     
    type I interferon signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    nuclear envelope NAS
    Non-traceable Author Statement
    more info
    PubMed 
    nuclear replication fork IEA
    Inferred from Electronic Annotation
    more info
     
    oligosaccharyltransferase complex IEA
    Inferred from Electronic Annotation
    more info
     
    protein-DNA complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    three-prime repair exonuclease 1
    Names
    3' repair exonuclease 1
    3'-5' exonuclease TREX1
    DNase III
    deoxyribonuclease III
    NP_009179.2
    NP_338599.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009820.2 RefSeqGene

      Range
      5401..6816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_007248.5NP_009179.2  three-prime repair exonuclease 1 isoform c

      See identical proteins and their annotated locations for NP_009179.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The resulting isoform (c) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AC134772, AF319566, AF319569, AJ243797, BT020053, W24304
      Consensus CDS
      CCDS59451.1
      UniProtKB/Swiss-Prot
      Q9NSU2
      UniProtKB/TrEMBL
      Q5TZT0
      Related
      ENSP00000415972.1, ENST00000444177.1
      Conserved Domains (1) summary
      cl10012
      Location:4201
      DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily
    2. NM_033629.6NP_338599.1  three-prime repair exonuclease 1 isoform b

      See identical proteins and their annotated locations for NP_338599.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The resulting isoform (b) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AF319569, AL137745, BT020053
      Consensus CDS
      CCDS2769.1
      UniProtKB/Swiss-Prot
      Q9NSU2
      Related
      ENSP00000486676.2, ENST00000625293.3
      Conserved Domains (1) summary
      cl10012
      Location:14211
      DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      48465830..48467645
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016381.5: Suppressed sequence

      Description
      NM_016381.5: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    2. NM_033627.3: Suppressed sequence

      Description
      NM_033627.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which represents a rare readthrough event.
    3. NM_033628.2: Suppressed sequence

      Description
      NM_033628.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which represents a rare readthrough event.
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